|Note: Some of the information on this page is for our legacy systems only. The page is scheduled for an update to make it applicable to Graham.|
|Description: Bayesian estimation of phylogeny|
|SHARCNET Package information: see MrBAYES software page in web portal|
|Full list of SHARCNET supported software|
MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. MrBayes uses Markov chain Monte Carlo (MCMC) methods to estimate the posterior distribution of model parameters.
Kraken and Requin have the newer version:
module load mrbayes/3.2.2
In Angel, Brown, Goblin, Hound, Iqaluk, Monk, Orca, Redfin, Saw, Wobbie, only 3.1.2 version can be used.
module load mrbayes/3.1.2
The MrBayes job can be submitted in a batch file which indicates both the Nexus file and your settings. The batch file(e.g batch.txt) should be located in the same dictionary with the Nexus file.
sqsub -r 1h -o my.out mb batch.txt
A MrBayes batch file is done by adding a MRBAYES block to a Nexus file, either the same file containing the DATA block or a separate Nexus file. The MrBayes block simply contains the commands as you would have given them from the command line, with the difference that each command line is ended with a semi-colon. For instance, a MrBayes block that performs three single-run analyses of the dataset primates.nex and stores each result in a separate file is given below:
begin mrbayes; set autoclose=yes nowarn=yes; execute primates.nex; lset nst=6 rates=gamma; mcmc nruns=1 ngen=10000 samplefreq=10 file=primates.nex1; mcmc file=primates.nex2; mcmc file=primates.nex3; end;
The "batch.txt" file containing this text above will be used as an Nexus file.
If you need a newer version of MrBayes, please submit a ticket or send email to firstname.lastname@example.org
o MrBayes Homepage